chr9-85242868-C-G

Variant names:

• chr9-85242868-C-G
• rs10512160

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0312 in 152,276 control chromosomes in the GnomAD database, including 68 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.031 (68 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.428
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0312 (4748/152276) while in subpopulation SAS AF = 0.0458 (221/4822). AF 95% confidence interval is 0.0409. There are 68 homozygotes in GnomAd4. There are 2388 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 68 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0312 AC: 4742 AN: 152158 Hom.: 68 Cov.: 33

Gnomad AFR AF: 0.0372

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0188

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.0156

Gnomad SAS AF: 0.0460

Gnomad FIN AF: 0.0428

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0294

Gnomad OTH AF: 0.0316

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0312 AC: 4748 AN: 152276 Hom.: 68 Cov.: 33 AF XY: 0.0321 AC XY: 2388 AN XY: 74466

African (AFR) AF: 0.0373 AC: 1550 AN: 41562

American (AMR) AF: 0.0188 AC: 287 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0190 AC: 66 AN: 3472

East Asian (EAS) AF: 0.0154 AC: 80 AN: 5180

South Asian (SAS) AF: 0.0458 AC: 221 AN: 4822

European-Finnish (FIN) AF: 0.0428 AC: 454 AN: 10604

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0294 AC: 1999 AN: 68016

Other (OTH) AF: 0.0313 AC: 66 AN: 2112

Alfa AF: 0.0301 Hom.: 9

Bravo AF: 0.0294

Asia WGS AF: 0.0280 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.0
DANN	Benign	0.76
PhyloP100		0.43

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10512160; hg19: chr9-87857783;